Orphan sections are sections present in the input files which are not explicitly placed into the output file by the linker script. The linker will still copy these sections into the output file, but it has to guess as to where they should be placed. The linker uses a simple heuristic to do this. It attempts to place orphan sections after non-orphan sections of the same attribute, such as code vs data, loadable vs non-loadable, etc. If there is not enough room to do this then it places at the end of the file.
For ELF targets, the attribute of the section includes section type as well as section flag.